The Cobra is definitely a stronger package to begin with, but it depends on the extent of mods you want to do and what you'll be using the car for.
If you want to build a lot of horse power and drag race, the IRS is not the best choice. If you really want a Cobra, a 96-98 could be a good choice with the DOHC and live axle.
Basically, I had the same dilemma as you when I was getting ready to buy a car, and I decided on the GT. This is mainly because I planned on getting major suspension mods for handling and didn't want to pay the extra for the Cobra suspension just to change everything (although the Cobra motor is nice with its aluminum block and forged crank).
Also, I like to drag race from time to time and didn't want to mess with the IRS.
For the extra money that the Cobra costs (marked up to almost $40K) where I live, I think a $3K supercharger and $5K in suspension goes a long way towards having a GT that will thrash a stock Cobra for less money.
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2000GT Atlantic Blue: Cobra R Wheels-17x9 255/40/17, 17x10.5 315/35/17, tubular K-member & control arms, Tokico 5-ways, coil overs, sway bars, strut/shock tower bars, 70mm FMS throttle body, Saleen nose.
79 Pace Car: Maximum Motorsports suspension - H&R Race springs, Bilsteins, rear control arms, chassis bracing, Draglites, 302 w/ Edelbrock Performer intake, cam and 600cfm carb, BBK equal-lengths & H-pipe, 2.5" Flowmaster 2chmbr exhaust, Al Driveshaft, 8.8 trak-loc, TCI C4 w/ 2000 stall, B&M
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